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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
  • C12N15/1034—Isolating an individual clone by screening libraries
  • C12N15/1086—Preparation or screening of expression libraries, e.g. reporter assays
• • C—CHEMISTRY; METALLURGY
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
  • C12N15/1034—Isolating an individual clone by screening libraries
  • C12N15/1075—Isolating an individual clone by screening libraries by coupling phenotype to genotype, not provided for in other groups of this subclass
• • C—CHEMISTRY; METALLURGY
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  • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
  • C12N9/14—Hydrolases (3)
  • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
  • C12N9/22—Ribonucleases RNAses, DNAses

Definitions

• Object of the invention is a method and a DNA probe for preparation of restriction endonucleases, particularly those exhibiting desired sequential specificity.
• Restriction enzymes are proteins that cleave DNA molecule within or in the vicinity of a recognizable sequence. The sequence, understood as a definite sequence of nitrogen bases in the DNA molecule, determines whether cleavage of the molecule will occur or not.
• One restriction enzyme recognizes and cleaves one strictly defined DNA sequence. Restriction endonucleases are widely used research tools in contemporary molecular biology. At present, more than 3700 restriction endonucleases of type II are known, which specifically recognize 274 nucleotide sequences. This means that more than 80% theoretically possible specificities have not been up to now discovered in the nature [10].
• restriction endonucleases in genetic engineering and molecular diagnostics of hereditary diseases results in a growing demand for enzymes exhibiting new specificities. At the same time, mechanism of recognition of DNA sequence by enzymes is still poorly recognized which makes it impossible to employ methods of rational design in the field of engineering specificity.
• Targeted protein evolution is known, which is widely used for construction enzymes exhibiting new properties [4]. It consists in carrying out several rounds of mutagenesis and clones selection. The most efficient methods of protein evolution are based on in vitro cell-free compartmentalization systems (IVC).
• IVC in vitro cell-free compartmentalization systems
• a searched library of mutants of the protein being investigated is expressed by means of synthetic cellular extract in droplets of mineral oil having volumes of several femtolitres. Thanks to such a system, it is possible to detect enzymatic activity of a single protein molecule.
• a nonfluorescence substrate of the enzyme being investigated is transformed into a fluorescence product. This makes it possible to sort droplets using a fluorescence activated cell sorter (FACS) [6].
• FACS fluorescence activated cell sorter
• DNA is isolated which constitutes a matrix for a subsequent round of mutagenesis and selection. This allows to search through a library of 10 10 -10 12 clones during a single experiment. By comparison, classical in vivo screening methods make it possible to search through a library of about 10 6 clones [8].
• probes fluorescence markers of which are located on opposite endings of a DNA oligonucleotide (short sequence), whereas the sequence is recognized somewhere in the middle. From laws governing the FRET phenomenon it results that such probe must be short enough to obtain a suitable signal level, which in turn causes poor cleavage by enzymes and additionally impairs ability to detect their activity. Because of that, first restriction enzymes poorly ‘notice’ short fragments of DNA in which a measurable FRET level is still observed.
• the invention refers to a new method of detection of endonucleolytic activity within the desired DNA sequence and to a screening method of library of enzyme variants (mutants) in view of such activity.
• the method of the invention consists in applying a fluorescence-marked DNA probe for screening a library of mutants preferably in IVC format and/or in using other High Throughput Screening (HTS) technique, which is achieved through expression of proteins included in the library of mutants in a cell-free system in the presence and by means of the DNA probe, and then proteins thus obtained, resulting from expression of clones from the library, degrade the DNA probe if their specificity towards a substrate matches the searched one. Degradation of the DNA probe is detected as disappearance of FRET phenomenon between fluorescence markers included within the probe. After that, microcompartments in which the FRET phenomenon ceases to occur are separated from the remaining ones using Fluorescence Activated Cell Sorter (FACS) and/or other equipment for I-ITS analysis.
• FACS Fluorescence Activated Cell Sorter
• DNA coding clones capable of degrading the probe is amplified using Polymerase Chain Reaction (PCR) techniques is used as a basis for construction of the subsequent library of mutants, which is searched in the subsequent round of screening, according to the above-mentioned scheme, and the subsequent rounds of screening are carried out until an enzyme of desired properties is obtained.
• the library of mutants is a pool of DNA molecules coding various variants of proteins in such a manner that their expression in a cell-free system can occur.
• Expression in the cell-free system is achieved in microcompartments, the size of which is adjusted such that a single compartment includes one to at least several clones from the library of mutants.
• the DNA probe of the invention is characterized in that markers of the DNA probe are located in a direct vicinity of a sequence recognized by a searched restriction enzyme and/or in the vicinity of DNA restriction sites, and between the markers the FRET (Free Radiationless Energy Transfer) phenomenon occurs.
• FRET Free Radiationless Energy Transfer
• the state-of-the-art methods are either accurate and very slow—i.e. searching through a library of mutants by a research team takes at least several years, or are sufficiently fast and very rough—i.e. conditions for selection are too mild and too much improper results is qualified to subsequent rounds, and—as a final result—the whole process collapses because of an excess of cases erroneously taken as positive ones. Only a combination of a stringent selection and a possibility of a search through a huge library makes it possible to obtain restriction endonucleases of the desired sequential specificity.
• the invention makes it possible to obtain restriction endonucleases having new specificities toward substrates, not existing in the nature. Thanks to it, generating enzymes for molecular diagnostics using RFLP analysis is possible (polymorphism of a length of restriction fragments).
• RFLP analysis consists in digesting genetic material of a patient with restriction enzymes, and then separation of these fragments on agarose gel. Basing on a gel image, one can find whether a patient is a carrier of a mutation causing a particular genetic disease.
• the problem is a small number of enzymes recognizing DNA sequences that are significant from a diagnostic point of view. Thanks to possibility of generating such enzymes RFLP analysis can be applied to screening studies in a view of many genetic diseases.
• a use of the probe of the invention makes it possible to search efficiently through a sufficiently large library of clones, to find probably restriction endonucleases of the desired specificity.
• Location of markers in a direct vicinity of a recognizable sequence and/or a DNA cleavage site provides sufficiently stringent conditions for selection to keep at minimum an amount of cases erroneously regarded as recognizing the searched sequence.
• the probe of the invention provides a suitable level of selection and is well processed by the enzymes.
• the probe has markers located near to each other within a large fragment of DNA. The method of the invention is explained below in preferable examples of embodiments.
• Restriction endonuclease MvaI which recognizes CCWGG sequence (W is A or T), was selected as a core for mutagenesis.
• Amino acids participating in recognizing the DNA sequence: Y213, H223, D224, H225, R209, D207, T68, R230 and T102 were selected as a randomization target.
• a primary library of mutants was constructed by a method of combinatorial synthesis using ITERATETM technology supplied by Geneart company. About 10 12 unique clones were obtained.
• Each of the clones codes a sequence of a mutated gene of endonuclease MvaI under control of a promoter from bacteriophage T7, which makes it possible to express that gene in a cell-free system of protein synthesis.
• oligonucleotide 2 [SEQ ID NO: 2]
• TTGCATCAAAGCCTGAAAGGCGGCCATCCT oligonucleotide 2, [SEQ ID NO: 2]
• the resulting preparations of oligonucleotides 1 and 2 were suspended in a volume of 10 mM TrisHCl pH 8.0 suitable to obtain final concentration of 0.2 M. Then, equal volumes of solutions of oligonucleotides 1 and 2 were mixed together, heated to 95° C. for 5 minutes and cooled to 10° C. at the rate of 0.5° C. per minute.
• the resulting duplex of oligonucleotides was used as a DNA probe (Probe 1) in subsequent experiments.
• 0.5 ug DNA library was added to 50 ul of mixture for cell-free protein synthesis supplemented with the DNA probe at the final concentration of 0.02 M.
• the reaction mixture was added to 0.2 ml solution of the composition: 0.5% Triton-X100; 4.5% Span-80.
• the resulting mixture was emulsified while shaking at 1600 RPM for 5 minutes at 4° C.
• the subsequent aqueous phase in a form of 0.6 ml 2% Tween 80 in PBS was then added.
• the resulting mixture was shaken at 800 RPM for 2 minutes. As a result, a mixture of droplets of oil in the aqueous phase was obtained.
• each of the droplets one to several DNA molecules from a library of mutants, ten to twenty molecules of the probe and a set of substances necessary for in vitro translation and transcription to occur, were closed.
• the mixture was incubated for 3 hours at 37° C., to allow for protein expression and degradation of the DNA probe.
• the mixture of droplets was put onto the flow cytometer FACSAria II and separated while keeping the following parameters: die diameter 70 um, sorting rate 70000 events per second, wavelength of fluorescence excitation 480 nm, readout of fluorescence signal within the wavelength range 512-522 nm.
• the sorter selected droplets of the highest fluorescence. Altogether 96 droplets were collected, which were used for PCR reaction. Each of the droplets was placed in a different well of a 96-well polypropylene plate.
• DNA oligonucleotides were used as starters for the PCR reaction: T7F of the sequence ATGCGTCCGGCGTAGA and T7R of the sequence TATGCTAGTTATTGCTCAG. Polimerase Pfu Turbo (Staragene) were used for amplification.
• Each of the droplets was suspended in 5 ul 10 mM TrisHCl pH 8.0. The plate with suspended droplets was centrifuged at 13000 RPM for 15 minutes. The upper phase of oil was removed, whereas the aqueous phase was extracted with 2 ul diethyl ether, which was removed by evaporation under reduced pressure in a SpeedVac-type apparatus.
• DNA thus purified was suspended in a 10 ul mixture for PCR of the composition: 20 mM TrisHCl pH 8.8; 10 mM (NH 4 ) 2 SO 4 ; 10 mM KCl; 0.1% (v/v) Triton X-100; 0.1 mg/ml BSA; 0.125 mM each of dNTP; 0.5 uM starter T7F; 0.5 uM starter T7R; 0.5U polimerase Pfu Turbo.
• the PCR reaction was carried out in a thermocycler using the following program: 95° C.-3 minutes; (95° C.-30 sec.; 45° C. 35 sec; 72° C.-1 minute), while repeating 30 times operations listed in the parentheses; and 72° C.-10 minutes.
• the resulting DNA was purified from reaction mixtures using a set for DNA purification after enzymatic reactions “Clean-UP” (A&A Biotechnology). In this way, the amplified library of DNA clones coding restriction enzymes of sequential specificity TCAGG was obtained.
• the present example assumes additional increase of specificity of enzymes obtained during a process of selection through subsequent rounds of the process, in order to eliminate the primary sequential specificity of the enzyme which was a matrix to form the starting library of clones (in this case, the enzyme is restriction endonuclease MvaI of specificity CCWGG, where W is A or T).
• Example 2 The whole process is carried out in the same way as in Example 1 up to obtaining amplified library of 96 clones of coding enzymes of specificity TCAGG. They are used for generating material for the second round of selection by a method error-prone PCR.
• DNA of each of the clones included in the amplified library was mixed.
• the mixture was used as a matrix in PCR reaction of the following parameters.
• the following DNA oligonucleotides were used as starters for the PCR: T7F of the sequence ATGCGTCCGGCGTAGA [SEQ ID NO: 3] and T7R of the sequence TATGCTAGTTATTGCTCAG [SEQ ID NO: 4].
• composition of the reaction mixture 75 mM Tris-HCl (pH 8.8 at 25° C.); 20 mM (NH 4 ) 2 SO 4 ; 0.01% (v/v) Tween 20; 7mM MgCl 2 ; 0.5 mM MnCl 2 ; 1 mM dCTP; 0.2 mM dATP; 1 mM dTTP; 0.2 mM dGTP; 2.5 U recombined polimerase Taq (Fermentas); 10 uM starter T7F; 10 uM starter T7R.
• PCR reaction was carried out in a thermocycler using the following program: 95° C.-3 minutes; (95° C.-30 sec.; 45° C.-35 sec; 72° C.-2 minutes) while repeating 25 times operations listed in the parentheses; and 72° C.-10 minutes.
• an additional DNA probe (Probe 2) was used, including oligonucleotide 3 of the sequence: AGGATGGCCGCCTTCCAGGCTTTGATGCAA [SEQ ID NO: 5] marked at 5′-end with fluorescence colorant Cy5, and at 3′-end—with quencher
• the material obtained from the error-prone PCR reaction was subject to expression in a IVC system analogously to the material from the primary library of clones in Example 1, the difference being that both probe 1 and probe 2 were present in the reaction mixture. Both the probes were used at the concentration of 0.02 M.
• the mixture of droplets was put onto a flow cytometer FACSCAria II and separated while keeping the following parameters: die diameter 70 um, sorting rate 8 000 events per second.
• the cytometer worked in 2 readout channels. In the first channel, readout of a signal of the probe 1 was collected. The wavelength of fluorescence excitation was 480 nm, whereas a readout of a fluorescence signal was carried out within the wavelength range 512-522 nm. In the second channel, a parallel readout of a signal of the probe 2 was made. The wavelength of fluorescence excitation was 635 nm, whereas a readout of a fluorescence signal was carried out within the wavelength range 655-695 nm.
• the sorter selected droplets of the highest fluorescence within the wavelength range 512-522 nm and, at the same time, of the minimum fluorescence within the wavelength range 655-695. Altogether 20 droplets were collected, which were used for the PCR reaction analogous to that in Example 1. The resulting DNA was used as a matrix for the subsequent error-prone PCR and after selection 10 DNA clones coding restriction endonucleases of sequential specificity TCAGG free from original specificity of enzyme MvaI (CCWGG) were obtained.

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• 2009
  • 2009-09-28 PL PL389135A patent/PL389135A1/pl unknown
• 2010
  • 2010-09-28 US US13/498,584 patent/US20130005582A1/en not_active Abandoned
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